ClinVar Genomic variation as it relates to human health
NM_014989.7(RIMS1):c.1889G>A (p.Arg630Gln)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_014989.7(RIMS1):c.1889G>A (p.Arg630Gln)
Variation ID: 1018375 Accession: VCV001018375.6
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6q13 6: 72237854 (GRCh38) [ NCBI UCSC ] 6: 72947557 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 14, 2021 Feb 14, 2024 Jun 13, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014989.7:c.1889G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055804.2:p.Arg630Gln missense NM_001168407.2:c.311G>A NP_001161879.1:p.Arg104Gln missense NM_001168408.2:c.311G>A NP_001161880.1:p.Arg104Gln missense NM_001168409.2:c.68G>A NP_001161881.1:p.Arg23Gln missense NM_001168410.2:c.266G>A NP_001161882.1:p.Arg89Gln missense NM_001350414.2:c.311G>A NP_001337343.1:p.Arg104Gln missense NM_001350415.2:c.311G>A NP_001337344.1:p.Arg104Gln missense NM_001350416.2:c.311G>A NP_001337345.1:p.Arg104Gln missense NM_001350417.2:c.311G>A NP_001337346.1:p.Arg104Gln missense NM_001350418.2:c.311G>A NP_001337347.1:p.Arg104Gln missense NM_001350419.2:c.311G>A NP_001337348.1:p.Arg104Gln missense NM_001350420.2:c.311G>A NP_001337349.1:p.Arg104Gln missense NM_001350421.2:c.242G>A NP_001337350.1:p.Arg81Gln missense NM_001350422.2:c.311G>A NP_001337351.1:p.Arg104Gln missense NM_001350423.2:c.311G>A NP_001337352.1:p.Arg104Gln missense NM_001350424.2:c.242G>A NP_001337353.1:p.Arg81Gln missense NM_001350425.2:c.311G>A NP_001337354.1:p.Arg104Gln missense NM_001350426.2:c.311G>A NP_001337355.1:p.Arg104Gln missense NM_001350427.2:c.311G>A NP_001337356.1:p.Arg104Gln missense NM_001350428.2:c.242G>A NP_001337357.1:p.Arg81Gln missense NM_001350429.2:c.311G>A NP_001337358.1:p.Arg104Gln missense NM_001350430.2:c.242G>A NP_001337359.1:p.Arg81Gln missense NM_001350431.2:c.311G>A NP_001337360.1:p.Arg104Gln missense NM_001350432.2:c.311G>A NP_001337361.1:p.Arg104Gln missense NM_001350433.2:c.311G>A NP_001337362.1:p.Arg104Gln missense NM_001350434.2:c.311G>A NP_001337363.1:p.Arg104Gln missense NM_001350435.2:c.311G>A NP_001337364.1:p.Arg104Gln missense NM_001350436.2:c.311G>A NP_001337365.1:p.Arg104Gln missense NM_001350437.2:c.242G>A NP_001337366.1:p.Arg81Gln missense NM_001350438.2:c.311G>A NP_001337367.1:p.Arg104Gln missense NM_001350439.2:c.311G>A NP_001337368.1:p.Arg104Gln missense NM_001350440.2:c.311G>A NP_001337369.1:p.Arg104Gln missense NM_001350441.2:c.311G>A NP_001337370.1:p.Arg104Gln missense NM_001350442.2:c.311G>A NP_001337371.1:p.Arg104Gln missense NM_001350443.2:c.311G>A NP_001337372.1:p.Arg104Gln missense NM_001350444.2:c.311G>A NP_001337373.1:p.Arg104Gln missense NM_001350445.2:c.311G>A NP_001337374.1:p.Arg104Gln missense NM_001350446.2:c.311G>A NP_001337375.1:p.Arg104Gln missense NM_001350447.2:c.311G>A NP_001337376.1:p.Arg104Gln missense NM_001350448.2:c.311G>A NP_001337377.1:p.Arg104Gln missense NM_001350449.2:c.311G>A NP_001337378.1:p.Arg104Gln missense NM_001350450.2:c.242G>A NP_001337379.1:p.Arg81Gln missense NM_001350452.2:c.311G>A NP_001337381.1:p.Arg104Gln missense NM_001350454.2:c.311G>A NP_001337383.1:p.Arg104Gln missense NM_001350455.2:c.311G>A NP_001337384.1:p.Arg104Gln missense NM_001350456.2:c.311G>A NP_001337385.1:p.Arg104Gln missense NM_001350457.2:c.311G>A NP_001337386.1:p.Arg104Gln missense NM_001350458.2:c.311G>A NP_001337387.1:p.Arg104Gln missense NM_001350459.2:c.242G>A NP_001337388.1:p.Arg81Gln missense NM_001350460.2:c.311G>A NP_001337389.1:p.Arg104Gln missense NM_001350461.2:c.68G>A NP_001337390.1:p.Arg23Gln missense NM_001350462.2:c.242G>A NP_001337391.1:p.Arg81Gln missense NM_001350463.2:c.68G>A NP_001337392.1:p.Arg23Gln missense NM_001350464.2:c.68G>A NP_001337393.1:p.Arg23Gln missense NM_001350465.2:c.68G>A NP_001337394.1:p.Arg23Gln missense NM_001350466.2:c.68G>A NP_001337395.1:p.Arg23Gln missense NM_001350467.2:c.68G>A NP_001337396.1:p.Arg23Gln missense NM_001350468.2:c.68G>A NP_001337397.1:p.Arg23Gln missense NM_001350469.2:c.68G>A NP_001337398.1:p.Arg23Gln missense NM_001350470.2:c.266G>A NP_001337399.1:p.Arg89Gln missense NM_001350471.2:c.242G>A NP_001337400.1:p.Arg81Gln missense NM_001350472.2:c.266G>A NP_001337401.1:p.Arg89Gln missense NM_001350473.2:c.266G>A NP_001337402.1:p.Arg89Gln missense NM_001350474.2:c.266G>A NP_001337403.1:p.Arg89Gln missense NC_000006.12:g.72237854G>A NC_000006.11:g.72947557G>A NG_016209.1:g.355908G>A - Protein change
- R104Q, R23Q, R630Q, R81Q, R89Q
- Other names
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- Canonical SPDI
- NC_000006.12:72237853:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00003
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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RIMS1 | Little evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1131 | 1177 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (1) |
criteria provided, single submitter
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Jun 13, 2022 | RCV001317664.6 |
Submissions - Germline
Classification
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The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Jun 13, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV001508334.4
First in ClinVar: Mar 14, 2021 Last updated: Feb 14, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1018375). This variant has not been reported in the literature in individuals affected with RIMS1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 630 of the RIMS1 protein (p.Arg630Gln). (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs1351490013 ...
HelpRecord last updated Feb 14, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.